Judging by the amount of maps/mods made per game these days, I'd say JKA has a larger audience. That being said, I reckon you're more likely to find a 'playable' server on JK2, as it seems like it's more the 'players' that hang out there now ('players' as opposed to the JKA/AOL chatroom crowd).

There are 'real' servers for both games of course, but it's a question of knowing where they are. Whenever I use the in-game browser in JKA, I can't find a real game for love nor money. So I tend to go for either bots or direct-connection games; easier for me